Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3′ v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Support for 5′ reagents is new in Cell Ranger 2.1.

The subsequent steps vary depending on how many samples, libraries, and flowcells you have. We will describe them in order of increasing complexity:

This is the most basic case. You have a single biological sample, which was prepared into a single library, and then sequenced on a single flowcell. Assuming the FASTQs have been generated with
cellranger mkfastq
, you just need to run
cellranger count
as described in
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.

If you have a library which was sequenced across multiple flowcells (e.g. to increase sequencing saturation), you can pool the reads from both sequencing runs. Follow the steps in
Specifying Input Fastqs
to combine them in a single
cellranger count
run.

This comprises two scenarios.

If you prepared multiple libraries from the same sample (technical replicates, for example), then each one should be run through a separate instance of
cellranger count
. Once those are completed, you can perform a combined analysis using
cellranger aggr
, as described in
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. (This is illustrated in the figure).

If you prepared multiple libraries from the same sample and want to pool them and analyze the combined data as a single sample, then you will need to use the
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to treat the multiple libraries as coming from a single sample. (This is not illustrated in the figure).

Array-CGH

Mature B-cell neoplasms arise in B-cells that have entered germinal centers within lymph nodes as part of the immune response. They display great heterogeneity at the clinical, pathologic, and genetic levels and represent 6-7% and 5-6% of all new estimated cancer cases and deaths respectively in the US in 2009. They are the fifth most common neoplasm in both males and females, and of the 103,960 estimated new cases in 2009, 20,860 comprise diffuse large B-cell lymphoma (DLBCL), 20,580 multiple myeloma (MM), 15,490 chronic lymphocytic leukemia /small lymphocytic lymphoma (CLL/SLL), 14,900 follicular lymphoma (FL), 8,510 Hodgkin’s lymphoma (HL), 6,000 marginal zone lymphomas (MZL) (including the three subtypes: extranodal marginal zone of mucosa-associated lymphoid tissue [MALT], nodal marginal zone, and splenic marginal zone), and 3,730 mantle cell lymphomas (MCL), as the major subtypes. With the exclusion of HL, 32,520 deaths are expected in 2009 in the US as a result of these neoplasms.

Diagnosis of these neoplasms relies mostly on the pathologic examination of biopsy material, be it either of an incisional or excisional biopsy of a suspect lymph node, a fine needle aspirate of a suspect lymph node (as yet to be considered adequate for initial diagnosis, unless it is the only safe option), or a bone marrow aspirate. Unlike other cancers, rarely are other biopsy/surgical procedures performed prior to the initiation of treatment, thus limiting the amount of tissue available for diagnostic and prognostic purposes. CGI has optimized the utility of array-CGH so that it can be routinely applied to the study of a range of specimen types including formalin-fixed paraffin-embedded (FFPE) specimens, often the only specimen available for analysis.

CGI has designed an oligonucleotide-based array (MatBA®) for the detection of gains and losses in mature B-cell neoplasms for utilization within a clinical laboratory.

For CLL/SLL, it’s primary value is in routine prognostication, and as an assay, has been approved in the CGI Diagnostic Laboratory by both CLIA and New York State. In this disease where approximately 50% patients have an aggressive course and 50% can live for many years without requiring treatment, robust prognostication is highly desirable. Together with
IGHV
mutation status, theMatBA®-CLL Array-CGH test provides important genetic-based information to guide clinical management of this disease.

I am interested in understanding how cancer cells ‘switch off’ the normal immune response in acute myeloid leukaemia with the aim of developing novel immunotherapeutic strategies.

I am currently developing several research projects:

I started work in the Haemato-Oncology department in the Barts Cancer Institute in October 2011 as part of John Gribben’s cancer immunotherapy group. I developed my research interests as an MRC Clinical Training Fellow in the group between 2005 and 2009 when I investigated T cells in acute myeloid leukaemia. I gained experience in immunomagnetic cell separation, flow cytometry, gene expression profiling and confocal microscopy of the immune synapse.

I developed a technique for separating T cells from the peripheral blood of patients presenting with AML that was published in the
Journal of Immunological Methods
in 2009 and my data characterising T cell defects in AML was published in
Blood
in the same year. I left Barts in 2009 to complete my clinical haematology training which included a year spent at the Hammersmith Hospital as a stem cell transplant coordinator. During this time, I gained valuable experience in the organisation as well as inpatient and outpatient management of patients undergoing allogeneic stem cell transplantation.

I now plan to develop as an independent researcher taking forward my basic science research examining T cell function in haematologic malignancy to investigate new immunotherapeutic strategies in AML.

The AMI (Apparatus for Meridian Identification)works by monitoring the electrical conductivity and capacity at specific acupoints at the tip of fingers and toes (called Sei point, or Jing/Well points). After years of research, Dr. Motoyama was able to show that there is a close correlation between the electrical conductivity of meridians and the flow of Ki (or Chi) in the meridians. The basic research Dr. Motoyama did to support his claim about the AMI can be found in his book “
Measurement of Ki Energy Diagnoses Treatment: Treatment Principle of Oriental Medicine from an Electrophysiological Viewpoints”
published by Human Science Press in 1977. Please see below (Dr. Motoyama’s Findings using the AMI)for the pages from this book.

The AMI measures the electrical conductivity, capacitance, and polarization of skin tissue and fluids; it uses these to evaluate the tissue condition and the functioning of the acupuncture meridians and their corresponding internal organs.

The AMI data tells you:

● The condition of the meridians and the functioning of their corresponding internal organs – lung, large intestine, heart, small intestine, spleen, liver, stomach, urinary bladder, kidney and gall bladder; ● Whether your Ki energy is excessive or deficient ; ● An objective analysis of your autonomic nervous system; ● The effects of acupuncture, meditation, and exercise through continuous monitoring of the autonomic nervous system and Ki energy; ● Chakra type, meaning which chakra is most active/inactive. The data cannot measure the amount of energy in the chakra quantitatively but can indicate which one is activated at the moment.